Contacts of the strand formed by residues 411 - 430 (chain B) in PDB entry 2W77
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 411 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B GLN* 3.9 37.9 - - + +
403B GLU* 5.2 7.4 - - + +
404B HIS 3.5 10.3 - - - +
405B ASN* 4.3 19.5 - - - +
406B PHE* 4.4 0.4 - - - -
409B GLY 4.2 9.4 - - - +
410B TRP* 1.3 77.4 - - - +
412B GLY* 1.3 69.2 + - - +
413B LYS* 5.4 0.7 - - + -
460B TYR* 4.1 1.2 - - + +
461B LEU* 3.5 6.5 - - - +
462B THR* 2.9 44.4 + - + +
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Residues in contact with GLY 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B GLU* 3.3 5.2 - - - +
404B HIS* 3.0 35.8 + - - -
406B PHE* 4.0 9.1 - - - -
411B VAL* 1.3 76.4 - - - +
413B LYS* 1.3 61.2 + - - -
414B VAL* 5.9 0.2 - - - -
460B TYR 3.3 10.8 - - - -
461B LEU* 3.7 12.6 - - - -
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Residues in contact with LYS 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLN* 4.7 9.8 - - - +
137B LEU* 3.2 33.3 - - - +
272B LYS* 5.5 5.1 - - - +
401B ASN* 3.9 24.8 - - + +
402B LEU 3.4 10.3 - - - +
403B GLU* 3.4 31.7 + - + +
411B VAL* 5.4 0.2 - - + -
412B GLY* 1.3 75.1 - - - +
414B VAL* 1.3 73.3 + - - +
415B GLN* 3.9 12.7 - - + +
458B ASP 3.6 2.0 - - - +
459B ILE* 3.4 3.6 - - - +
460B TYR* 3.0 72.7 + - + +
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Residues in contact with VAL 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ALA 3.6 1.0 - - - +
401B ASN* 3.2 6.8 + - - +
402B LEU* 2.9 46.5 + - + +
412B GLY 5.9 0.2 - - - -
413B LYS* 1.3 77.9 - - - +
415B GLN* 1.3 67.2 + - - +
416B LEU* 4.0 22.5 - - + +
457B LEU* 4.4 13.0 - - + -
458B ASP 3.6 3.4 - - - -
459B ILE* 4.3 18.6 - - + -
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 5.3 2.6 - - - +
157B ARG* 4.3 17.6 - - - +
220B ASP* 3.5 29.5 + - - +
221B GLY* 4.9 1.2 - - - -
222B ILE* 3.8 31.6 - - + +
400B ALA 3.3 5.6 - - - +
401B ASN* 3.5 25.5 + - - +
413B LYS* 3.9 24.0 - - + +
414B VAL* 1.3 73.9 - - - +
416B LEU* 1.3 64.6 + - - +
417B ASP* 4.9 4.9 - - - +
456B SER 4.4 0.7 - - - -
457B LEU* 3.6 9.4 - - - +
458B ASP* 3.0 34.9 + - + +
460B TYR* 4.6 3.7 - - + -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B VAL 4.7 0.2 - - - -
399B PHE* 3.1 4.7 - - - -
400B ALA* 2.6 57.2 + - + +
414B VAL* 4.0 18.8 - - + -
415B GLN* 1.3 79.2 - - - +
417B ASP* 1.3 66.9 + - - +
456B SER 3.5 5.8 - - - +
457B LEU* 4.4 13.2 - - + -
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Residues in contact with ASP 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 4.8 2.1 - - - +
222B ILE* 3.6 33.4 - - + +
270B ARG* 4.4 8.5 + - - -
397B THR* 4.0 13.7 - - + +
398B VAL 3.7 1.1 - - - -
399B PHE* 3.3 16.6 - - - +
415B GLN* 4.9 4.2 - - - +
416B LEU* 1.3 85.9 + - - +
418B HIS* 1.3 62.2 + - - +
419B LYS* 5.1 6.5 - - + +
454B SER 3.2 1.4 - - - +
455B ASN* 3.2 9.3 + - - -
456B SER* 2.9 45.1 + - - +
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Residues in contact with HIS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B ARG 3.8 0.5 - - - +
397B THR* 3.4 6.3 - - - -
398B VAL* 2.8 55.2 + - + +
417B ASP* 1.3 73.5 - - - +
419B LYS* 1.3 60.3 + - - +
420B ILE* 4.7 6.2 - - + +
453B LYS* 4.5 16.2 - - + +
454B SER 3.4 2.9 - - - -
455B ASN* 3.0 29.6 - - - +
1819B PO4 2.8 46.7 + - - -
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Residues in contact with LYS 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B TYR* 3.5 42.7 - - + -
224B SER* 4.0 14.9 + - - +
235B ASN* 4.4 0.2 + - - -
395B THR* 4.9 11.2 - - - -
396B ARG 3.7 2.0 - - - +
397B THR* 3.3 32.1 - - + +
417B ASP* 4.0 6.9 - - + +
418B HIS* 1.3 74.7 - - - +
420B ILE* 1.3 67.8 + - - +
421B ASN* 3.3 29.8 + - - +
452B THR 3.3 1.2 - - - +
453B LYS* 3.2 7.3 - - - -
454B SER* 2.8 49.4 + - - +
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B TYR* 3.9 18.8 - - + -
395B THR* 3.1 6.4 - - - -
396B ARG* 2.8 63.7 + - + +
418B HIS* 4.7 5.8 - - + +
419B LYS* 1.3 79.9 - - - +
421B ASN* 1.3 69.3 + - - +
451B GLU* 3.1 39.9 - - + +
452B THR 3.3 2.5 - - - +
453B LYS* 4.4 13.0 - - + -
1819B PO4 3.3 34.1 - - - +
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Residues in contact with ASN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B SER* 4.7 0.5 + - - -
226B ALA* 3.8 28.5 + - + +
233B ALA* 3.1 32.0 + - + +
235B ASN* 3.9 19.4 + - - +
394B TYR 3.6 4.3 - - - -
395B THR* 3.8 9.3 - - - +
419B LYS* 3.3 33.1 + - - +
420B ILE* 1.3 74.8 - - - +
422B GLY* 1.3 58.6 + - - +
423B TYR* 5.3 1.6 - - - -
451B GLU 3.6 0.9 - - - -
452B THR* 2.9 37.1 + - - +
454B SER* 5.6 0.9 + - - -
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Residues in contact with GLY 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ALA* 3.8 8.3 - - - +
393B GLN* 3.6 3.5 - - - -
394B TYR* 2.7 59.0 + - - +
420B ILE 4.1 0.2 - - - -
421B ASN* 1.3 73.7 - - - +
423B TYR* 1.3 62.9 + - - +
450B GLY 3.4 11.7 - - - -
451B GLU* 4.1 2.0 - - - -
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Residues in contact with TYR 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B TYR* 3.3 48.7 - + + -
232B SER 3.6 18.4 - - - +
233B ALA* 4.6 4.3 - - + -
391B TRP* 4.1 8.5 - + + +
392B GLU 3.4 10.3 - - - +
394B TYR* 4.0 6.8 - - - -
421B ASN 5.3 1.1 - - - -
422B GLY* 1.3 76.0 - - - -
424B HIS* 1.3 61.1 + - - +
425B ALA* 4.7 2.2 - - + -
448B TYR* 3.1 38.6 - - + -
449B THR* 3.2 11.2 + - - -
450B GLY* 3.0 62.5 + - - +
451B GLU* 4.5 1.1 - - - -
452B THR* 5.7 1.3 - - - -
485B TRP* 3.1 29.4 + + - -
487B GLY* 4.2 4.3 - - - -
488B LYS 5.1 0.4 + - - -
522B ILE* 4.6 1.0 - - - +
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Residues in contact with HIS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B SER* 4.3 1.4 + - - -
392B GLU* 3.0 49.6 + - + +
394B TYR* 5.3 3.4 - - + -
423B TYR* 1.3 73.9 - - - +
425B ALA* 1.3 58.1 + - - +
426B PRO* 3.3 18.1 - - + +
447B LYS* 4.0 12.6 + - - -
448B TYR 3.9 2.0 - - - -
449B THR* 4.3 17.7 - - + +
1816B PO4 3.6 21.0 + - - -
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390B SER 3.1 9.6 - - - +
391B TRP* 3.9 31.9 - - + +
423B TYR* 5.1 1.1 - - + -
424B HIS* 1.3 73.9 - - - +
426B PRO* 1.3 59.9 - - - +
427B LEU* 3.4 18.6 + - + +
446B GLN 3.6 1.2 - - - +
447B LYS* 3.0 4.5 - - - -
448B TYR* 2.7 49.0 + - + +
449B THR* 4.5 1.0 - - - +
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Residues in contact with PRO 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B TRP* 3.9 7.0 - - + +
389B SER* 3.6 5.4 - - - -
390B SER* 3.1 36.3 + - - +
424B HIS* 3.3 23.1 - - + +
425B ALA* 1.3 83.0 - - - +
427B LEU* 1.3 59.5 + - - +
446B GLN 3.9 0.2 - - - +
447B LYS* 3.4 20.4 - - + -
515B TRP* 3.5 17.7 - - + -
1816B PO4 3.4 34.5 - - - +
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Residues in contact with LEU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B SER* 4.7 4.3 - - - -
361B GLY 5.0 2.9 - - - +
362B TRP* 3.6 46.9 - - + +
388B TRP* 3.9 3.1 - - - -
389B SER* 3.4 8.3 - - - +
390B SER 3.9 19.1 - - - +
391B TRP* 3.9 33.0 - - + +
425B ALA* 3.8 12.1 - - + +
426B PRO* 1.3 74.4 - - - +
428B GLY* 1.3 59.3 + - - +
445B ALA* 3.4 1.8 - - - -
446B GLN 2.9 32.7 + - - +
448B TYR* 3.7 28.3 - - + -
515B TRP* 3.6 5.5 - - - -
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Residues in contact with GLY 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B GLY* 3.4 1.9 - - - -
386B ALA* 2.7 26.6 + - - +
388B TRP* 3.7 19.4 - - - -
389B SER* 3.2 13.1 + - - -
427B LEU* 1.3 75.6 - - - +
429B ALA* 1.3 62.3 + - - +
443B ILE* 4.1 7.0 - - - -
444B VAL 3.4 10.3 - - - -
445B ALA* 4.1 3.4 - - - -
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B GLY 4.5 0.4 - - - -
362B TRP* 3.8 40.4 - - + +
384B ASN* 3.4 10.8 - - - +
385B GLY* 3.7 13.2 - - - -
386B ALA 4.3 0.9 - - - +
428B GLY* 1.3 75.9 - - - +
430B ILE* 1.3 62.4 + - - +
431B MET* 3.3 5.9 + - + +
443B ILE* 3.3 7.6 - - - +
444B VAL* 3.0 32.4 + - - +
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Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B PRO* 4.2 11.6 - - + +
382B PHE* 4.6 1.6 - - + -
384B ASN* 2.7 41.4 + - + +
429B ALA* 1.3 70.7 - - - +
431B MET* 1.3 63.8 + - - +
434B TRP* 4.2 10.1 - - + -
441B ALA* 4.2 20.4 - - + -
442B LYS 3.6 11.0 - - - +
443B ILE* 3.1 25.4 - - + -
500B THR* 4.4 2.9 - - + -
503B PHE* 4.1 32.1 - - + -
506B TRP* 3.5 41.1 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il